LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide

units		real
atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style	pppm 0.0001

read_data	data.peptide
Reading data file ...
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 2 by 2 MPI processor grid
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     7 = max # of 1-3 neighbors
    14 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.011 seconds

neighbor	2.0 bin
neigh_modify	delay 5

timestep	2.0

group		peptide type <= 12
84 atoms in group peptide
group		one id 2 4 5 6
4 atoms in group one
group		two id 80 82 83 84
4 atoms in group two
group		ref id 37
1 atoms in group ref
group		colvar union one two ref
9 atoms in group colvar

fix		1 all nvt temp 275.0 275.0 100.0 tchain 1

shell "rm -f peptide2.colvars.*"
fix		2 all colvars peptide.colvars2 output peptide2
----------------------------------------------------------------------
Initializing the collective variables module, version 2025-04-30.
Please cite Fiorin et al, Mol Phys 2013:
  https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Summary of compile-time features available in this build:
  - C++ language version: 201703
  - Multiple replicas: not available
  - Lepton custom functions: available
  - Tcl interpreter: not available
Using LAMMPS interface, version "2025-03-31".

fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
      19 = # of size 2 clusters
       6 = # of size 3 clusters
       3 = # of size 4 clusters
     640 = # of frozen angles
  find clusters CPU = 0.000 seconds

#dump		1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id

thermo_style	custom step temp etotal pe ke epair ebond f_2
thermo		10


run		100
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars2":
# units = "" [default]
# smp = "cvcs" [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
  Initializing a new collective variable.
  # name = "one"
    Initializing a new "distance" component.
    # name = "" [default]
    # componentCoeff = 1 [default]
    # componentExp = 1 [default]
    # period = 0 [default]
    # wrapAround = 0 [default]
    # forceNoPBC = off [default]
    # scalable = on [default]
      Initializing atom group "group1".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group1" defined with 4 atoms requested.
      Initializing atom group "group2".
      # name = "" [default]
      # centerToOrigin = off [default]
      # centerToReference = off [default]
      # rotateToReference = off [default]
      # atomsOfGroup = "" [default]
      # indexGroup = "" [default]
      # psfSegID =  [default]
      # atomsFile = "" [default]
      # dummyAtom = ( 0 , 0 , 0 ) [default]
      # enableFitGradients = on [default]
      # printAtomIDs = off [default]
      Atom group "group2" defined with 4 atoms requested.
    # oneSiteSystemForce = off [default]
    # oneSiteTotalForce = off [default]
  All components initialized.
  # timeStepFactor = 1 [default]
  # width = 1 [default]
  # lowerBoundary = 0 [default]
  # upperBoundary = 1 [default]
  # hardLowerBoundary = on [default]
  # hardUpperBoundary = off [default]
  # expandBoundaries = off [default]
  # extendedLagrangian = off [default]
  # outputValue = on [default]
  # outputVelocity = off [default]
  # outputTotalForce = off [default]
  # outputAppliedForce = off [default]
  # subtractAppliedForce = off [default]
  # runAve = off [default]
  # corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 1 in total.
----------------------------------------------------------------------
  Initializing a new "harmonic" instance.
  # name = "h_pot"
  # colvars = { one }
  # stepZeroData = off [default]
  # outputEnergy = off [default]
  # outputFreq = 1000 [default]
  # timeStepFactor = 1 [default]
  # writeTISamples = off [default]
  # writeTIPMF = off [default]
  # centers = { 10 }
  # targetCenters = { 10 } [default]
  # outputCenters = off [default]
  # forceConstant = 100
  # decoupling = off [default]
  # targetForceConstant = -1 [default]
  The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 0, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
The final output state file will be "peptide2.colvars.state".
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
SHAKE stats (type/ave/delta/count) on step 0
Bond:    4   1.111     1.44264e-05        9
Bond:    6   0.996998  7.26967e-06        6
Bond:    8   1.08      1.32536e-05        7
Bond:   10   1.111     1.22749e-05        8
Bond:   12   1.08      1.11767e-05        9
Bond:   14   0.96      0                  1
Bond:   18   0.957206  4.37979e-05     1280
Angle:  31   104.519   0.00396029       640
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
   Step          Temp          TotEng         PotEng         KinEng         E_pair         E_bond          f_2      
         0   282.10052     -5237.458      -6372.3765      1134.9186     -6442.7679      16.557152      273.74323    
        10   333.47919     -4982.3966     -6324.0167      1341.6201     -6400.422       21.367762      12.393263    
        20   309.56902     -4999.498      -6244.9251      1245.4271     -6401.6983      43.59542       13.004313    
        30   316.9763      -5025.5662     -6300.7936      1275.2273     -6422.5376      27.323196      6.7589588    
        40   297.55779     -5088.2203     -6285.325       1197.1047     -6395.3749      13.6769        25.625023    
        50   296.79994     -5117.2966     -6311.3524      1194.0558     -6451.8308      30.631241      5.3320864    
        60   281.72778     -5188.4971     -6321.9161      1133.419      -6427.8858      26.287725      20.574037    
        70   277.26052     -5224.8434     -6340.2902      1115.4468     -6447.8521      27.742891      0.6942037    
        80   268.01485     -5281.8507     -6360.1013      1078.2505     -6496.6085      20.300755      5.2607208    
        90   270.43474     -5334.0836     -6422.0696      1087.986      -6563.2513      39.846097      1.1832275    
SHAKE stats (type/ave/delta/count) on step 100
Bond:    4   1.11096   0.000191462        9
Bond:    6   0.996989  3.55509e-05        6
Bond:    8   1.08      9.0997e-06         7
Bond:   10   1.111     1.58544e-05        8
Bond:   12   1.08      5.80604e-06        9
Bond:   14   0.959997  0                  1
Bond:   18   0.957198  2.92445e-05     1280
Angle:  31   104.52    0.00239923       640
       100   260.35636     -5387.2284     -6434.6681      1047.4396     -6534.1956      20.246866      0.075048501  
Saving collective variables state to "peptide2.colvars.state".
Loop time of 0.25089 on 4 procs for 100 steps with 2004 atoms

Performance: 68.875 ns/day, 0.348 hours/ns, 398.581 timesteps/s, 798.757 katom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.17444    | 0.17908    | 0.18253    |   0.8 | 71.38
Bond    | 0.00021455 | 0.00050755 | 0.00085023 |   0.0 |  0.20
Kspace  | 0.018422   | 0.022097   | 0.026823   |   2.3 |  8.81
Neigh   | 0.035293   | 0.03531    | 0.035343   |   0.0 | 14.07
Comm    | 0.0065644  | 0.0067089  | 0.0069318  |   0.2 |  2.67
Output  | 0.0001271  | 0.00014806 | 0.00020638 |   0.0 |  0.06
Modify  | 0.0065706  | 0.0065796  | 0.0065976  |   0.0 |  2.62
Other   |            | 0.0004623  |            |       |  0.18

Nlocal:            501 ave         513 max         494 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost:         6572.5 ave        6593 max        6548 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs:         177058 ave      181778 max      174301 min
Histogram: 2 0 0 0 1 0 0 0 0 1

Total # of neighbors = 708234
Ave neighs/atom = 353.41018
Ave special neighs/atom = 2.3403194
Neighbor list builds = 13
Dangerous builds = 1

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Colvars module (Fiorin2013, plus other works listed for specific features)


% Colvars module:
% Colvars-LAMMPS interface:
% Harmonic colvar bias implementation:
% Optimal rotation via flexible fitting:
% distance colvar component:

@article{Fiorin2013,
  author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
  title = {Using collective variables to drive molecular dynamics simulations},
  journal = {Mol. Phys.},
  year = {2013},
  volume = {111},
  number = {22-23},
  pages = {3345--3362},
  publisher = {Taylor & Francis},
  doi = {10.1080/00268976.2013.813594},
  url = {https://doi.org/10.1080/00268976.2013.813594}
}


% LAMMPS engine:

@article{Thompson2022,
  title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
  author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
  journal = {Comp. Phys. Comm.},
  volume = {271},
  pages = {108171},
  year = {2022},
  doi = {10.1016/j.cpc.2021.108171},
  url = {https://doi.org/10.1016/j.cpc.2021.108171}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Total wall time: 0:00:00
